Computerized screening of G-protein coupled receptors to identify and characterize olfactory receptors

Olfactory receptors (ORs) are a group of G protein coupled receptors (GPCRs) that initiate chemical odorant signals. Although ORs are predominantly located in nasal epithelia to detect smell, these receptors are also present in peripherally in non-nasal organs/tissues. Since the quality of life and cognitive and sensorial features of sense of smell are worsened in multiple chemical sensitivity due to the interaction of ORs with offending compounds, it is important to not only differentiate these receptors from other GPCRs but also characterize these organelles to understand the underlying mechanisms of smelling disorders. The aim of this study was develop computerized programs to differentiate ORs from GPCRs. The computer program was developed on the basis of widely accepted basic algorithms. It is noteworthy that an accuracy of 95.5% was attained, a level not achieved using other established techniques for screening of ORs from GPCRs. The high accuracy rate indicates that this method of differential identification appears reliable. Our findings indicate that this novel method may be considered as a tool for identification and characterization of receptors which might aid in therapeutic approaches to human chemical-mediated sensitization.

FPGA-based distributed computing microarchitecture for complex physical dynamics investigation

In this paper, we present a distributed computing system, called DCMARK, aimed at solving partial differential equations at the basis of many investigation fields, such as solid state physics, nuclear physics, and plasma physics. This distributed architecture is based on the cellular neural network paradigm, which allows us to divide the differential equation system solving into many parallel integration operations to be executed by a custom multiprocessor system. We push the number of processors to the limit of one processor for each equation. In order to test the present idea, we choose to implement DCMARK on a single FPGA, designing the single processor in order to minimize its hardware requirements and to obtain a large number of easily interconnected processors. This approach is particularly suited to study the properties of 1-, 2- and 3-D locally interconnected dynamical systems. In order to test the computing platform, we implement a 200 cells, Korteweg-de Vries (KdV) equation solver and perform a comparison between simulations conducted on a high performance PC and on our system. Since our distributed architecture takes a constant computing time to solve the equation system, independently of the number of dynamical elements (cells) of the CNN array, it allows us to reduce the elaboration time more than other similar systems in the literature. To ensure a high level of reconfigurability, we design a compact system on programmable chip managed by a softcore processor, which controls the fast data/control communication between our system and a PC Host. An intuitively graphical user interface allows us to change the calculation parameters and plot the results.

Image processing with cellular nonlinear networks implemented on field-programmable gate arrays for real-time applications in nuclear fusion

In the past years cameras have become increasingly common tools in scientific applications. They are now quite systematically used in magnetic confinement fusion, to the point that infrared imaging is starting to be used systematically for real-time machine protection in major devices. However, in order to guarantee that the control system can always react rapidly in case of critical situations, the time required for the processing of the images must be as predictable as possible. The approach described in this paper combines the new computational paradigm of cellular nonlinear networks (CNNs) with field-programmable gate arrays and has been tested in an application for the detection of hot spots on the plasma facing components in JET. The developed system is able to perform real-time hot spot recognition, by processing the image stream captured by JET wide angle infrared camera, with the guarantee that computational time is constant and deterministic. The statistical results obtained from a quite extensive set of examples show that this solution approximates very well an ad hoc serial software algorithm, with no false or missed alarms and an almost perfect overlapping of alarm intervals. The computational time can be reduced to a millisecond time scale for 8 bit 496560-sized images. Moreover, in our implementation, the computational time, besides being deterministic, is practically independent of the number of iterations performed by the CNN-unlike software CNN implementations.

Estimating nonlinear interdependences in dynamical systems using cellular nonlinear networks

We propose a method for estimating nonlinear interdependences between time series using cellular nonlinear networks. Our approach is based on the nonlinear dynamics of interacting nonlinear elements. We apply it to time series of coupled nonlinear model systems and to electroencephalographic time series from an epilepsy patient, and we show that an accurate approximation of symmetric and asymmetric realizations of a nonlinear interdependence measure can be achieved, thus allowing one to detect the strength and direction of couplings.

Real-time neural network inversion on the SRC-6e reconfigurable computer

Implementation of real-time neural network inversion on the SRC-6e, a computer that uses multiple field-programmable gate arrays (FPGAs) as reconfigurable computing elements, is examined using a sonar application as a specific case study. A feedforward multilayer perceptron neural network is used to estimate the performance of the sonar system (Jung et al., 2001). A particle swarm algorithm uses the trained network to perform a search for the control parameters required to optimize the output performance of the sonar system in the presence of imposed environmental constraints (Fox et al., 2002). The particle swarm optimization (PSO) requires repetitive queries of the neural network. Alternatives for implementing neural networks and particle swarm algorithms in reconfigurable hardware are contrasted. The final implementation provides nearly two orders of magnitude of speed increase over a state-of-the-art personal computer (PC), providing a real-time solution.

Image processing for a tactile/vision substitution system using digital CNN

In view of the parallel processing and easy implementation properties of CNN, we propose to use digital CNN as the image processor of a tactile/vision substitution system (TVSS). The digital CNN processor is used to execute the wavelet down-sampling filtering and the half-toning operations, aiming to extract important features from the images. A template combination method is used to embed the two image processing functions into a single CNN processor. The digital CNN processor is implemented on an intellectual property (IP) and is implemented on a XILINX VIRTEX II 2000 FPGA board. Experiments are designated to test the capability of the CNN processor in the recognition of characters and human subjects in different environments. The experiments demonstrates impressive results, which proves the proposed digital CNN processor a powerful component in the design of efficient tactile/vision substitution systems for the visually impaired people.